An introduction to best practices in free energy calculations

Methods in Molecular Biology
Michael R Shirts, David L Mobley

Abstract

Free energy calculations are extremely useful for investigating small-molecule biophysical properties such as protein-ligand binding affinities and partition coefficients. However, these calculations are also notoriously difficult to implement correctly. In this chapter, we review standard methods for computing free energy via simulation, discussing current best practices and examining potential pitfalls for computational researchers performing them for the first time. We include a variety of examples and tips for how to set up and conduct these calculations, including applications to relative binding affinities and small-molecule solvation free energies.

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Related Concepts

Thermodynamics
Ethanol
Ligand Binding
Methane
Biophysical Processes
Biophysics
Solvents

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